Strain identifier

BacDive ID: 132079

Type strain: Yes

Species: Actinobaculum massiliense

Strain Designation: FC1, FC3

Strain history: <- S. Khelaifia, Timone Hospital, Marseille, France; FC3 <- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes

NCBI tax ID(s): 202789 (species)

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General

@ref: 23870

BacDive-ID: 132079

DSM-Number: 100580

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, coccus-shaped, colony-forming

description: Actinobaculum massiliense FC1 is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from urine, 12-year-old patient with acute cystitis.

NCBI tax id

  • NCBI tax id: 202789
  • Matching level: species

strain history

  • @ref: 23870
  • history: <- S. Khelaifia, Timone Hospital, Marseille, France; FC3 <- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes

doi: 10.13145/bacdive132079.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinobaculum
  • species: Actinobaculum massiliense
  • full scientific name: Actinobaculum massiliense corrig. Greub and Raoult 2002

  • synonyms

    • @ref: 20215
    • synonym: Actinobaculum massiliae

@ref: 23870

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinobaculum

species: Actinobaculum massiliense

full scientific name: Actinobaculum massiliense Greub and Raoult 2006

strain designation: FC1, FC3

type strain: yes

Morphology

cell morphology

  • @ref: 43943
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 43943
  • type of hemolysis: alpha
  • hemolysis ability: 1
  • colony size: 0.5-1.5 mm
  • colony color: pale-grey
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Columbia agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23870PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
43943Columbia agaryes5% blood enriched

culture temp

@refgrowthtypetemperaturerange
23870positivegrowth37mesophilic
43943positiveoptimum37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43943anaerobe
43943microaerophile

spore formation

  • @ref: 43943
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4394329864mannitol-builds acid from
4394337684mannose-builds acid from
4394316634raffinose-builds acid from
4394330911sorbitol-builds acid from
4394328017starch-builds acid from
4394327082trehalose-builds acid from
439434853esculin-hydrolysis
439435291gelatin-hydrolysis
4394317632nitrate-reduction
4394317234glucose+builds acid from
4394317306maltose+builds acid from
4394333942ribose+builds acid from
4394318222xylose+builds acid from
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivegroup IDis resistant
439432676amoxicillinyesyes
43943amoxicillinyesyes10
4394348947clavulanic acidyesyes10
43943204928cefotaximeyesyes
4394329007ceftriaxoneyesyes
43943471744imipenemyesyes
4394345924trimethoprimyesyes26
439439332sulfamethoxazoleyesyes26
4394348923erythromycinyesyes
4394350845doxycyclineyesyes
4394328001vancomycinyesyes
4394328915fosfomycinyesyes
4394328077rifampicinyesyes
4394317833gentamicinyesyes
43943100241ciprofloxacinyesyes
4394337943colistinyesyes

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
43943catalase-1.11.1.6
43943cytochrome oxidase-1.9.3.1
43943leucine arylamidase+3.4.11.1
43943alpha-glucosidase+3.2.1.20
43943beta-glucuronidase+3.2.1.31
43943pyrazinamidase+/-3.5.1.B15
43943beta-galactosidase+/-3.2.1.23
43943pyrrolidonyl arylamidase-3.4.19.3
43943alkaline phosphatase-3.1.3.1
43943urease-3.5.1.5
43943alpha-galactosidase-3.2.1.22
43943N-acetyl-beta-glucosaminidase-3.2.1.52
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
23870---+/--+--+/---------+/-++++-+++--+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
23870urine, 12-year-old patient with acute cystitisFranceFRAEurope
43943urine of a 12-year-old patient suffering from acute cystitis2015-04-15

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host Body Product#Fluids#Urine
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_1698.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_247;96_965;97_1124;98_1340;99_1698&stattab=map
  • Last taxonomy: Actinobaculum massiliense subclade
  • 16S sequence: LN870313
  • Sequence Identity:
  • Total samples: 1977
  • soil counts: 31
  • aquatic counts: 21
  • animal counts: 1924
  • plant counts: 1

Safety information

risk assessment

  • @ref: 23870
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23870
  • description: Actinobaculum massiliense partial 16S rRNA gene, strain FC3
  • accession: LN870313
  • length: 1501
  • database: ena
  • NCBI tax ID: 202789

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinobaculum massiliense FC3GCA_001457435scaffoldncbi202789
66792Actinobaculum massiliense FC32811995073draftimg202789

GC content

  • @ref: 23870
  • GC-content: 60.17
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.838yes
gram-positiveyes92.513no
anaerobicyes80.443no
aerobicno93.209yes
halophileno72.107no
spore-formingno96.23yes
glucose-utilyes87.15no
motileno94.25yes
thermophileno95.379no
glucose-fermentyes71.676no

External links

@ref: 23870

culture collection no.: DSM 100580, CSUR P1982

literature

  • topic: Phylogeny
  • Pubmed-ID: 27117391
  • title: Description of strain FC3(T) as the neotype strain of Actinobaculum massiliense.
  • authors: Bakour S, Beye M, Raoult D, Fournier PE
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001110
  • year: 2016
  • mesh: Actinomycetaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Child, Cystitis/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
23870Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100580Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100580)
43943Sofiane Bakour, Mamadou Beye, Didier Raoult, Pierre-Edouard FournierDescription of strain FC3T as the neotype strain of Actinobaculum massiliense10.1099/ijsem.0.001110IJSEM 66: 2702-2703 201627117391
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68380Automatically annotated from API rID32A
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/